Are they compatible, or is there a compatibility patch anywhere for them? I've been looking around and can't find an answer. I don;t want to install fook while I have FWE running in case They aren't.

Thanks.

The current versions of FWE and FOOK2 are not compatible. There was a compatibility patch at one point, but many versions ago. I wouldn't recommend even attempting to run both together these days.

Out of the two, which would you say was better?

If I had to choose one or the other, I'd have to choose FOOK. I like the weapons in FOOK better than the ones from FWE.

I've managed to get them to work together though.
The only issues I have with it is there are some duplicate items...
FOOK Colt 1911 == FWE Colt .45
...stuff like that.
Also, Weapon Mod Kits will only work with one or the other, not both. I have WMK CP'ed to mod FOOK weapons, since like I said, I like FOOK's weapons better.

Get FWE if you want alternate starts (i.e. being a brotherhood outcast), a tougher overall game (which is also configurable in toughness), and some lore-friendly (imo) weapons. I prefer FWE due to these reasons. I used to use FOOK2, but it didn't have as many features for me as FWE did; FOOK2 added a lot of quality weapons though. A LOT of weapons. Its a FOOK staple, along with overhauling some areas (i.e. Megaton has some newer things in it).